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- PDB-3g25: 1.9 Angstrom Crystal Structure of Glycerol Kinase (glpK) from Sta... -

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Basic information

Entry
Database: PDB / ID: 3g25
Title1.9 Angstrom Crystal Structure of Glycerol Kinase (glpK) from Staphylococcus aureus in Complex with Glycerol.
ComponentsGlycerol kinase
KeywordsTRANSFERASE / Glycerol kinase / Glycerol / idp00743 / ATP-binding / Glycerol metabolism / Kinase / Nucleotide-binding / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


glycerol-3-phosphate metabolic process / glycerol kinase / glycerol kinase activity / glycerol metabolic process / glycerol catabolic process / ATP binding / cytosol
Similarity search - Function
Glycerol kinase / FGGY family of carbohydrate kinases signature 2. / Carbohydrate kinase, FGGY, conserved site / Carbohydrate kinase, FGGY / Carbohydrate kinase, FGGY, N-terminal / FGGY family of carbohydrate kinases, N-terminal domain / Carbohydrate kinase, FGGY, C-terminal / FGGY family of carbohydrate kinases, C-terminal domain / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain ...Glycerol kinase / FGGY family of carbohydrate kinases signature 2. / Carbohydrate kinase, FGGY, conserved site / Carbohydrate kinase, FGGY / Carbohydrate kinase, FGGY, N-terminal / FGGY family of carbohydrate kinases, N-terminal domain / Carbohydrate kinase, FGGY, C-terminal / FGGY family of carbohydrate kinases, C-terminal domain / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Glycerol kinase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus COL (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMinasov, G. / Skarina, T. / Onopriyenko, O. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 1.9 Angstrom Crystal Structure of Glycerol Kinase (glpK) from Staphylococcus aureus in Complex with Glycerol.
Authors: Minasov, G. / Skarina, T. / Onopriyenko, O. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJan 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycerol kinase
B: Glycerol kinase
C: Glycerol kinase
D: Glycerol kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,65028
Polymers225,8864
Non-polymers1,76424
Water21,1501174
1
A: Glycerol kinase
B: Glycerol kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,09718
Polymers112,9432
Non-polymers1,15416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7050 Å2
ΔGint-145 kcal/mol
Surface area33560 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15940 Å2
ΔGint-222 kcal/mol
Surface area64070 Å2
MethodPISA
3
C: Glycerol kinase
D: Glycerol kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,55310
Polymers112,9432
Non-polymers6108
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-69 kcal/mol
Surface area33720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.750, 193.742, 91.669
Angle α, β, γ (deg.)90.00, 103.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Glycerol kinase / ATP:glycerol 3-phosphotransferase / Glycerokinase / GK


Mass: 56471.402 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus COL (bacteria)
Strain: Staphylococcus aureus subsp. aureus COL / Gene: glpK, SACOL1320 / Plasmid: pMCSG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: Q5HGD2, glycerol kinase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1174 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1:1 v/v protein solution [10mg/ml protein, 0.3M NaCl, 10mM Na Hepes pH 7.5), screen solution (0.2M Na dihydrogen Phosphate , 20% PEG 3350, 6% Glycerol), VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.984 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 5, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 168279 / Num. obs: 168279 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 23.4 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 15.6
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 2.9 / Num. unique all: 8395 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.5.0051refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EZW

3ezw


Resolution: 1.9→44.81 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.921 / SU B: 8.765 / SU ML: 0.117 / TLS residual ADP flag: LIKELY RESIDUAL
Isotropic thermal model: Individual Atomic Isotropic Refinement
Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.168 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24562 8479 5 %RANDOM
Rwork0.19266 ---
all0.19529 159730 --
obs0.19529 159730 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.064 Å2
Baniso -1Baniso -2Baniso -3
1-4.41 Å20 Å20.58 Å2
2---2.76 Å20 Å2
3----1.37 Å2
Refinement stepCycle: LAST / Resolution: 1.9→44.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15703 0 96 1174 16973
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02217029
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211439
X-RAY DIFFRACTIONr_angle_refined_deg1.6791.94323160
X-RAY DIFFRACTIONr_angle_other_deg0.971327935
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.12852181
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.73224.861829
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.183152982
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0631596
X-RAY DIFFRACTIONr_chiral_restr0.1070.22471
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219549
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023523
X-RAY DIFFRACTIONr_mcbond_it1.4711.510397
X-RAY DIFFRACTIONr_mcbond_other0.5471.54307
X-RAY DIFFRACTIONr_mcangle_it2.175216808
X-RAY DIFFRACTIONr_scbond_it3.72336632
X-RAY DIFFRACTIONr_scangle_it5.3194.56341
LS refinement shellResolution: 1.903→1.952 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 599 -
Rwork0.235 11648 -
obs-11648 98.47 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3970.1070.05152.05350.08331.0325-0.0465-0.0090.0354-0.05910.03-0.0657-0.1767-0.04120.01650.03620.0164-0.00550.0502-0.00710.029713.653252.3019-2.982
20.84411.0071-0.14592.8781-0.27420.38640.0389-0.0792-0.01570.0673-0.0499-0.2111-0.04810.05880.0110.00760.0031-0.00890.1713-0.01820.172121.516731.38922.0717
30.51240.69130.22822.3143-0.17950.79920.0091-0.0687-0.07240.0764-0.0704-0.5236-0.10320.09210.06130.0178-0.0086-0.02180.2714-0.01750.320329.807333.36765.0514
40.67530.2719-0.30571.6715-0.64761.1847-0.08710.0474-0.07630.01310.0444-0.1480.1507-0.01870.04270.0326-0.01170.01130.1189-0.03290.1123-0.6239-11.412914.5586
51.29140.9227-0.52652.4038-0.7621.09350.03860.04210.1810.08920.03030.2914-0.0259-0.1487-0.06890.00340.00210.01090.21-0.00070.1716-1.722113.77295.7511
61.07680.8802-0.60322.1645-0.79121.0260.02510.12530.2560.04140.19920.48430.0191-0.2669-0.22430.0054-0.0079-0.00840.30880.0350.2412-13.42796.1596.8343
70.5632-0.1074-0.12731.0326-0.12840.98410.0378-0.01310.0554-0.0251-0.0126-0.1047-0.04090.0852-0.02520.01190.00130.00110.06340.00060.05283.219464.822833.3278
80.3155-0.28820.08641.8552-0.89131.05680.0576-0.0123-0.0211-0.1836-0.02480.04090.1755-0.0651-0.03280.0413-0.0048-0.02260.08770.00050.0596-9.909547.87939.7407
90.3634-0.0660.23041.3807-0.99531.47670.01460.0074-0.0124-0.09840.13480.26180.1364-0.2594-0.14940.0356-0.0048-0.02970.15160.00350.119-17.523149.180735.3089
100.6188-0.02050.06930.49610.48460.54540.0517-0.0307-0.02030.1001-0.02460.00570.1197-0.0221-0.02710.13290.0155-0.02570.04830.02510.0508-3.1290.262354.0066
110.5412-0.72660.44753.3363-1.0441.21830.1115-0.04080.0932-0.2378-0.0995-0.29760.11140.2075-0.0120.04590.0159-0.00660.1322-0.00970.15018.679719.159854.0915
120.5454-0.68030.1542.6544-0.1440.50880.1241-0.06730.0962-0.0577-0.0387-0.63450.0590.1414-0.08540.06290.0173-0.05260.2284-0.00490.284817.334616.921254.8594
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 245
2X-RAY DIFFRACTION2A246 - 396
3X-RAY DIFFRACTION3A397 - 498
4X-RAY DIFFRACTION4B0 - 303
5X-RAY DIFFRACTION5B304 - 404
6X-RAY DIFFRACTION6B405 - 498
7X-RAY DIFFRACTION7C1 - 242
8X-RAY DIFFRACTION8C243 - 396
9X-RAY DIFFRACTION9C397 - 498
10X-RAY DIFFRACTION10D1 - 239
11X-RAY DIFFRACTION11D240 - 396
12X-RAY DIFFRACTION12D397 - 498

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